Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01004962.1 Corchorus capsularis cultivar CVL-1 contig04980, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1845
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Found at i:751 original size:300 final size:300
Alignment explanation
Indices: 196--1781 Score: 1174
Period size: 330 Copynumber: 5.0 Consensus size: 300
186 GTTTTTCTTA
*
196 TTTTTT-T-AATTAATTTTTAATTAAATCGAAATAAGATTCA-AATCTTCGTAAAAACAAATCCT
1 TTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATTC-TCGTAAAAACAAATCCT
* * *
258 TAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATCTCAATGACTTTTGGCAACAAA
65 TAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTTGGCAACAAA
* *
323 AATCATGCAAAACTGAGCCGGGGCCCAGGAACACGTTTTTTGCCAAAACCTGTGATGGTTAGTAC
130 AATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAAACC-GTGATGGTTAGTAC
* * * *
388 ACGATTTCGGCT-AAATTTTACAAAAATTGACCTGAAAGATTTTTCCTTAATTTTTAGCCACAAT
194 ACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTCAGCCACAAT
*
452 AATCATAGGAATATATAATTCAACGTCAAAATGATTGAAGGC
259 AATCATAGAAATATATAATTCAACGTCAAAATGATTGAAGGC
* * *
494 TTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGGTACAGATTCTCGTAAAAACAAATTCTT
1 TTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATTCTCGTAAAAACAAATCCTT
* * *
559 AAATCCAATGTGTCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGACACTTGGCAACAAAA
66 AAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTTGGCAACAAAA
* * * *
624 ATTATGCAAAACTGAGTCGGGGCCCAGGATCGCGTTTTTGGCTAAAACTCGTGATGGTTAGTACA
131 ATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAAAC-CGTGATGGTTAGTACA
* *
689 CGAATTCGGCTAAAATTTTGCAAAAATAG-CCCGAAAGATTTTTCCTCAATTATTCA-CCACAAT
195 CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT-TTCAGCCACAAT
* * * *
752 ACTCAAAAAAATATATAATTCAACGCCAAAAAGATTGGAGGGCTTTTCAGACTTCTAAAATCGTT
259 AATCATAGAAATATATAATTCAACGTC--AAA-A-T-GA------TT--G--------AA--G--
**
817 TT
299 GC
* * *
819 TCTTATTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGATTCTGATGCTCGTAAAAACAAA
1 T-----TTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATTCTCGTAAAAACAAA
**
884 TCCTTAAATCCTTTGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTTGGCAA
61 TCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTTGGCAA
* * *
949 CCAAAATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTCGGCCAACACCCGTGATGGTTA
126 CAAAAATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAA-AACCGTGATGGTTA
*
1014 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAATTTT-AGCA
190 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTC-AATTTTCAGCC
1078 ACAATAATCATATGAAATATATAATTCAACGTCAAAATGATTGAAGGC
254 ACAATAATCATA-GAAATATATAATTCAACGTCAAAATGATTGAAGGC
* * * *** * * **
1126 TTTTTAACGCTTCAAATATCATTTTTCATATTTTTTCCTGAATTAA-TTTCTA-ACTAAATCG-A
1 TTTTT---TC-T-GAAT-TAATTTTT-A-ATTAAAT-C-GAAATAAGATTC-AGA-T-TCTCGTA
* * * * *
1188 AATAAGGTTCAGATTCTCGTAAAAACAAAT-T--CTTAA-ATCCAATGTGGCTGAGATTTGGTTA
53 AA-AA----CA-AATC-C-TTAAATCCAATGTGGC-TAAGAT----T-TGG-TTAGA--T-G--A
* * ** * ** **** * * * * * *
1249 GATGAATATACATATTTCAAG-GACTCTTAGCAATAAAAATTATGTAAAACAGAGTCGGGGCCGA
98 -AT--ATAGATAT-TTCAAGGACTCT-TGGCAAC-AAAAATCATGCAAAACTGAGCCGGGGCCCA
*
1313 GGAACGCGTTTTTGGCCAAAACCCGTGATGGTTAGAACACGATTTCGGCTAAAATTTTGCAAAAA
157 GGAACGCGTTTTTGGCCAAAA-CCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAA
* * * * * * *
1378 TTCACCCGAAAGATTATTCCTCAATTATTC-GCCACAGTACTCAAAAAAATATATAATTCAACGC
221 TTGACCCGAAAGATTTTTCCTCAATT-TTCAGCCACAATAATCATAGAAATATATAATTCAACGT
*
1442 CAAAAAGATTGGAGGGATTTCTGGTTTCTAAAATC
285 CAAAATGATT-GA---A-----GG----------C
* * *
1477 GTTTTTCTTATTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGATTCTGATGCTCGTAAAA
1 -----T-----TTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATTCTCGTAAAA
** *
1542 ACAAATCCTTAAATCCTTTGTGGCTAAGATTTGGTTAGAAGAATATAGATATTTCAAGGACTCTT
56 ACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTT
*
1607 GGCAACAAAACTCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAAACC------
121 GGCAACAAAAATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCGTGATG
* * * ** *
1666 -----CACACGATTTCGGCTAAAATTTTACAAAAATTGACCGGAAAGATTACTCCTCAATTTTTA
186 GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTCA
*
1726 GCAACAATAATCATAGGAAATATATAATTCAACGTCAAAATGATTGAAGGC
251 GCCACAATAATCATA-GAAATATATAATTCAACGTCAAAATGATTGAAGGC
1777 TTTTT
1 TTTTT
1782 CATGCTTCAA
Statistics
Matches: 1010, Mismatches: 156, Indels: 252
0.71 0.11 0.18
Matches are distributed among these distances:
290 4 0.00
295 1 0.00
298 6 0.01
299 1 0.00
300 224 0.22
301 22 0.02
302 7 0.01
303 1 0.00
304 1 0.00
305 3 0.00
306 1 0.00
307 4 0.00
308 6 0.01
309 2 0.00
310 6 0.01
311 9 0.01
312 10 0.01
313 6 0.01
315 1 0.00
317 7 0.01
318 70 0.07
319 29 0.03
320 6 0.01
321 5 0.00
322 3 0.00
323 5 0.00
325 2 0.00
326 1 0.00
327 2 0.00
328 2 0.00
329 5 0.00
330 249 0.25
331 47 0.05
332 67 0.07
333 119 0.12
334 2 0.00
335 1 0.00
336 1 0.00
337 1 0.00
340 4 0.00
341 5 0.00
342 1 0.00
343 6 0.01
344 2 0.00
345 6 0.01
346 5 0.00
350 5 0.00
351 11 0.01
352 5 0.00
353 4 0.00
354 1 0.00
355 6 0.01
356 4 0.00
357 1 0.00
358 1 0.00
361 4 0.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.32
Consensus pattern (300 bp):
TTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGATTCTCGTAAAAACAAATCCTT
AAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTTGGCAACAAAA
ATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCGTGATGGTTAGTACAC
GATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTCAGCCACAATAA
TCATAGAAATATATAATTCAACGTCAAAATGATTGAAGGC
Found at i:1269 original size:333 final size:331
Alignment explanation
Indices: 494--1845 Score: 1803
Period size: 330 Copynumber: 4.1 Consensus size: 331
484 GATTGAAGGC
* * * *
494 TTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGGTACAGATTCTCGTAAAAACAAATTCTT
1 TTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGGTTCAGATGCTCGTAAAAACAAATCCTT
* * *
559 AAATCCAATGTGTCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGACACTTGGCAACAAAA
66 AAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTTGGCAACAAAA
* * * * *
624 ATTATGCAAAACTGAGTCGGGGCCCAGGATCGCGTTTTTGGCTAAAACTCGTGATGGTTAGTACA
131 ATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCCGTGATGGTTAGTACA
* * * *
689 CGAATTCGGCTAAAATTTTGCAAAAATAG-CCCGAAAGATTTTTCCTCAATTATTCA-CCACAAT
196 CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTATTCCTCAATTATT-AGCAACAAT
* * *
752 ACTCAAAAAAATATATAATTCAACGCCAAAAAGATTGGAGGGC-TTTTCAGACTTCTAAAATCGT
260 AATCAAAAAAATATATAATTCAACGCCAAAAAGATTGGAAGGCTTTTTCAG-CTTCTAAAATCAT
*
816 TTTTCTTA
324 TTTTCATA
* *
824 TTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGATTCTGATGCTCGTAAAAACAAATCCTT
1 TTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGGTTCAGATGCTCGTAAAAACAAATCCTT
** *
889 AAATCCTTTGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTTGGCAACCAAA
66 AAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTTGGCAACAAAA
* *
954 ATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTCGGCCAACACCCGTGATGGTTAGTACA
131 ATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCCGTGATGGTTAGTACA
*
1019 CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAATT-TTAGCAACAAT
196 CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTATTCCTC-AATTATTAGCAACAAT
** * * *
1083 AATCATATGAAATATATAATTCAACGTCAAAATGATT-GAAGGCTTTTTAACGCTTC-AAATATC
260 AATCA-AAAAAATATATAATTCAACGCCAAAAAGATTGGAAGGCTTTTTCA-GCTTCTAAA-ATC
1146 ATTTTTCATA
322 ATTTTTCATA
* * *
1156 TTTTTTCCTGAATTAATTTCTAACTAAATCGAAATAAGGTTCAGATTCTCGTAAAAACAAATTCT
1 TTTTTT-CTGAATTAATTTCTAATTAAATCGAAATAAGGTTCAGATGCTCGTAAAAACAAATCCT
* * * *
1221 TAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATACATATTTCAAGGACTCTTAGCAATAAA
65 TAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTTGGCAACAAA
* * * * * *
1286 AATTATGTAAAACAGAGTCGGGGCCGAGGAACGCGTTTTTGGCCAAAACCCGTGATGGTTAGAAC
130 AATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCCGTGATGGTTAGTAC
* * * *
1351 ACGATTTCGGCTAAAATTTTGCAAAAATTCACCCGAAAGATTATTCCTCAATTATTCGCCACAGT
195 ACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTATTCCTCAATTATTAGCAACAAT
* * * * * * *
1416 ACTCAAAAAAATATATAATTCAACGCCAAAAAGATTGGAGGGATTTCT-GGTTTCTAAAATCGTT
260 AATCAAAAAAATATATAATTCAACGCCAAAAAGATTGGAAGGCTTTTTCAGCTTCTAAAATCATT
*
1480 TTTCTTA
325 TTTCATA
* *
1487 TTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGATTCTGATGCTCGTAAAAACAAATCCTT
1 TTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGGTTCAGATGCTCGTAAAAACAAATCCTT
** *
1552 AAATCCTTTGTGGCTAAGATTTGGTTAGAAGAATATAGATATTTCAAGGACTCTTGGCAACAAAA
66 AAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTTGGCAACAAAA
*
1617 CTCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCC------------ACA
131 ATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCCGTGATGGTTAGTACA
* * * *
1670 CGATTTCGGCTAAAATTTTACAAAAATTGACCGGAAAGATTACTCCTCAATTTTTAGCAACAATA
196 CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTATTCCTCAATTATTAGCAACAATA
** * *
1735 ATCATAGGAAATATATAATTCAACGTCAAAATGATT-GAAGGCTTTTTCATGCTTC-AAATATCA
261 ATCA-AAAAAATATATAATTCAACGCCAAAAAGATTGGAAGGCTTTTTCA-GCTTCTAAA-ATCA
1798 TTTTTCATA
323 TTTTTCATA
*
1807 -TTTTTCTGAATTAATTTCTAACTAAATCGAAATAAGGTT
1 TTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGGTT
Statistics
Matches: 899, Mismatches: 108, Indels: 41
0.86 0.10 0.04
Matches are distributed among these distances:
318 71 0.08
319 67 0.07
320 15 0.02
330 360 0.40
331 59 0.07
332 91 0.10
333 236 0.26
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.32
Consensus pattern (331 bp):
TTTTTTCTGAATTAATTTCTAATTAAATCGAAATAAGGTTCAGATGCTCGTAAAAACAAATCCTT
AAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTTGGCAACAAAA
ATCATGCAAAACTGAGCCGGGGCCCAGGAACGCGTTTTTGGCCAAAACCCGTGATGGTTAGTACA
CGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTATTCCTCAATTATTAGCAACAATA
ATCAAAAAAATATATAATTCAACGCCAAAAAGATTGGAAGGCTTTTTCAGCTTCTAAAATCATTT
TTCATA
Done.